6O96 Structural Protein Dna Transferase date Mar 13, 2019
title Dot1l Bound To The H2bk120 Ubiquitinated Nucleosome
authors M.I.Valencia-Sanchez, P.E.De Ioannes, W.Miao, N.Vasilyev, R.Chen E.Nudler, J.P.Armache, K.J.Armache
compound source
Molecule: Histone H3.2
Chain: A, E
Engineered: Yes
Mutation: Yes
Organism_scientific: Xenopus Laevis
Organism_common: African Clawed Frog
Organism_taxid: 8355
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Histone H4
Chain: B, F
Engineered: Yes

Organism_scientific: Xenopus Laevis
Organism_common: African Clawed Frog
Organism_taxid: 8355
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Histone H2a
Chain: C, G
Engineered: Yes
Mutation: Yes

Organism_scientific: Xenopus Laevis
Organism_common: African Clawed Frog
Organism_taxid: 8355
Gene: Hist1h2aj, Loc494591, Xelaev_18003602mg
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Histone H2b 1.1
Chain: D, H
Synonym: H2b1.1
Engineered: Yes
Mutation: Yes

Organism_scientific: Xenopus Laevis
Organism_common: African Clawed Frog
Organism_taxid: 8355
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Dna (146-Mer)
Chain: I
Engineered: Yes

Organism_scientific: Synthetic Construct
Organism_taxid: 32630
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Dna (146-Mer)
Chain: J
Engineered: Yes

Organism_scientific: Synthetic Construct
Organism_taxid: 32630
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Histone-Lysine N-Methyltransferase, H3 Lysine-79
Chain: K
Synonym: Dot1-Like Protein,Histone H3-K79 Methyltransferase Hmtase,Lysine N-Methyltransferase 4;
Ec: 2.1.1.43
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Dot1l, Kiaa1814, Kmt4
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Polyubiquitin-B
Chain: L
Engineered: Yes
Mutation: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ubb
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 1
R_factor
R_Free
crystal
cell
length a length b length c angle alpha angle beta angle gamma
1.000 1.000 1.000 90.00 90.00 90.00
method Electron Microscopyresolution 3.50 Å
ligand SAH enzyme Transferase E.C.2.1.1.43 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, E


C, G


F, B


H, D


K


Primary referenceStructural Basis of Dot1L Stimulation by Histone H2B Lysine 120 Ubiquitination., Valencia-Sanchez MI, De Ioannes P, Wang M, Vasilyev N, Chen R, Nudler E, Armache JP, Armache KJ, Mol Cell. 2019 Apr 8. pii: S1097-2765(19)30233-3. doi:, 10.1016/j.molcel.2019.03.029. PMID:30981630
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (275 Kb) [Save to disk]
  • Biological Unit Coordinates (6o96.pdb1.gz) 269 Kb
  • LPC: Ligand-Protein Contacts for 6O96
  • CSU: Contacts of Structural Units for 6O96
  • Retrieve 6O96 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6O96 from S2C, [Save to disk]
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  • Visual 3D analysis of 6O96
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  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 6o96 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6o96_K] [6o96_E] [6o96_I] [6o96_G] [6o96_D] [6o96_L] [6o96_C] [6o96_A] [6o96_H] [6o96_B] [6o96_F] [6o96_J]
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  • Domain organization of by SWISSPFAM
  • Other resources with information on 6O96
  • Community annotation for 6O96 at PDBWiki (http://pdbwiki.org)

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